Pigeon genome gives a picture of diversity

January 30, 2013This article courtesy of Nature News.

Humans shaped domestic pigeons into hundreds of breeds of various shapes, colors, and attributes — a diversity that captivated Charles Darwin, who even conducted breeding experiments on his own pigeons. Now, the genome of the rock pigeon Columba livia has been sequenced for the first time, giving scientists a resource for studying the genetics of how these traits evolved.

The study, published online today by Science, gives insight into both “fancy” domestic breeds and plain street pigeons. "We go from having virtually no genetic or genomic resources available for the pigeon to being able to map regions associated with particular traits,” says first author Michael Shapiro, a biologist at the University of Utah in Salt Lake City.

Shapiro partnered with Jun Wang at BGI-Shenzhen in China and scientists at the University of Copenhagen in Denmark, who sequenced a reference genome based on DNA from a breed called the Danish tumbler. The researchers then re-sequenced the genomes of 40 additional pigeons representing 36 different fancy breeds and two feral birds from different regions of the United States.

The study fills in knowledge about the relationships between breeds, many of which are centuries old with origins in the Middle East. Darwin argued that all fancy pigeon breeds descended from the rock pigeon. Shapiro says this study puts data behind that argument, as all breeds are more similar genetically to one another than to a closely related species of pigeon. It also found that street pigeons are genetically similar to racing homers, which frequently escape into the wild.

One question is whether similar traits in different breeds, such as flouncy leg feathers or short beaks, are caused by the same genetic mutations. The researchers analyzed head crests, feathers growing in reverse direction that vary from short tufts to outrageous manes that envelop the head. Inheritance studies by pigeon breeders suggested head crests were caused by a simple recessive trait. Using software developed for finding genes underlying human diseases, the researchers analyzed crested and uncrested breeds, and discovered a mutation in a gene called EphB2 that matched the crests in all cases. They believe the mutation evolved just once in the species.

Head crests, Shapiro said, are “one of many traits that we see in domestic pigeons that have a correlate in lots of natural species of birds,” where they are used in courtship and displays of aggression. Further research can discover whether the same gene is involved in creating crests in nature. In similar fashion, Shapiro says, scientists can use pigeon genetics to study the emergence of more complex traits.

Leif Andersson, a researcher at Uppsala University in Sweden who studies domestic animal genetics, says that the paper addresses a gap in knowledge about pigeons, which has lagged behind that of chickens, pigs, and dogs. Together, domestic species are important tools for comparative genomics, with traits honed by humans over thousands of years. “The different domestic animals complement each other,” he says, “because they've been selected for different purposes.”